Just bought Stellaris a few days ago. The first time I saved (to the cloud) and shut it down, my saves disappeared when I restarted the game. After playing a new game for a while, they reappeared. A bit of experimenting later, I discover that I can get my saves to reappear by starting a new game and immediately saving it. Once that's done, I can load my old save and proceed as normal.

Anyone have any idea what's going on or how to solve it?

cloud saves?
ironman mode = Documents\Paradox Interactive\Stellaris\pops_filestorage\save games

if you use this mode and have 'cloud saves' option on Galaxy then this folder will sync at the end of your game... assuming you are signed into Paradox account which is now required

if the above is true then you start a new session by pressing the 'continue' option it will start again from scratch because Paradox and Gog fucked up the launcher i.e, didn't test things actually work before kicking them out to paying customers

what does work is starting a game from the launcher [sign in required] then wait at least a min [two in Australia] for the network to sync all the way over to Paradox servers then your game save will show up and be highlighted in green instead of red or orange

I had the same problem.

I fixed it by logging into my Paradox account after launching the Paradox Launcher via Gog, but prior to launching Stellaris proper.